L7_TwoDyeGeneExp

L7_TwoDyeGeneExp - ECEN 689 Statistical Computation in GSP

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Unformatted text preview: ECEN 689 Statistical Computation in GSP http://www.ece.tamu.edu/~ulisses/ECEN689/ Lecture 7: Two-Dye Gene-Expression Microarrays Ulisses Braga-Neto Genomic Signal Processing Laboratory Department of Electrical and Computer Engineering Texas A&M University Competitive Hybridization • Labeled mRNA from distinct samples are hybridized on the same slide. • Two distinct channels: – Dye 1: cyanine 3 (cy3) - typical emission wavelength = 532 nm (green) – Dye 2: cyanine 5 (cy5) - typical emission wavelength = 635 nm (red) • Ratios of cy3/cy5 are taken, which cancels any spot effects across the array. • Recent two-dye arrays (e.g. Agilent) allow the analysis of each channel separately. Oligo Two-Dye Arrays • Probes are "long oligo" (e.g. 60-base) cDNAs (as opposed to the "short oligo" 25-base probes in Affymetrix arrays). • Only one long oligo probe per gene. • Longer oligo probes may have free extremeties closer to the solution phase, easing the hybridization process. Agilent Microarrays • Long-oligo Arrays built by ink- jet "in situ" deposition proprietary technology. Data Files • .GAL : Contains probe addressing information, control IDs and geometry information (similar to .CDF files in Affymetrix) • .GPR : Expression file output by GenePix image analysis software....
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This note was uploaded on 02/08/2010 for the course ECEN 689-601 taught by Professor Staff during the Spring '10 term at Texas A&M.

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L7_TwoDyeGeneExp - ECEN 689 Statistical Computation in GSP

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